Whether it's right or not running Windows application on Linux, there is a baby project that aims to compete with Wine.

Longene is an open source computer operating system kernel project that allows with a kernel modification to run programs and hardware drivers made for Windows operating systems natively on Linux. The difference between Longene and Wine is that it renders the Linux Kernel binary-compatible with non-Linux programs and drivers, no need to use emulation software like Wine.

The project is still under development and currently can be installed only on Ubuntu and Fedora. I think if this project sees the light, Microsoft will try to make Windows run natively Linux software, who knows! For more information about this project, check their main website here.

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